Maaslin2 - "Multivariable Association Discovery in Population-scale Meta-omics Studies"

MaAsLin2 is comprehensive R package for efficiently determining multivariable association between clinical metadata and microbial meta'omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods. MaAsLin2 is the next generation of MaAsLin.

Last updated 13 days ago

metagenomicssoftwaremicrobiomenormalizationbiobakerybioconductordifferential-abundance-analysisfalse-discovery-ratemultiple-covariatespublicrepeated-measurestools

10.37 score 123 stars 5 packages 484 scripts

MicrobiotaProcess - A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

MicrobiotaProcess is an R package for analysis, visualization and biomarker discovery of microbial datasets. It introduces MPSE class, this make it more interoperable with the existing computing ecosystem. Moreover, it introduces a tidy microbiome data structure paradigm and analysis grammar. It provides a wide variety of microbiome data analysis procedures under the unified and common framework (tidy-like framework).

Last updated 19 days ago

visualizationmicrobiomesoftwaremultiplecomparisonfeatureextractionmicrobiome-analysismicrobiome-data

9.35 score 182 stars 1 packages 129 scripts

DirichletMultinomial - Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data

Dirichlet-multinomial mixture models can be used to describe variability in microbial metagenomic data. This package is an interface to code originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15, as discussed further in the man page for this package, ?DirichletMultinomial.

Last updated 1 months ago

immunooncologymicrobiomesequencingclusteringclassificationmetagenomics

8.84 score 11 stars 25 packages 119 scripts

InteractiveComplexHeatmap - Make Interactive Complex Heatmaps

This package can easily make heatmaps which are produced by the ComplexHeatmap package into interactive applications. It provides two types of interactivities: 1. on the interactive graphics device, and 2. on a Shiny app. It also provides functions for integrating the interactive heatmap widgets for more complex Shiny app development.

Last updated 9 months ago

softwarevisualizationsequencinginteractive-heatmaps

8.49 score 129 stars 4 packages 132 scripts

microViz - Microbiome Data Analysis and Visualization

Microbiome data visualization and statistics tools built upon phyloseq.

Last updated 5 days ago

microbiomemicrobiome-analysismicrobiota

6.78 score 105 stars 1 packages 428 scripts

microbiomeMarker - microbiome biomarker analysis toolkit

To date, a number of methods have been developed for microbiome marker discovery based on metagenomic profiles, e.g. LEfSe. However, all of these methods have its own advantages and disadvantages, and none of them is considered standard or universal. Moreover, different programs or softwares may be development using different programming languages, even in different operating systems. Here, we have developed an all-in-one R package microbiomeMarker that integrates commonly used differential analysis methods as well as three machine learning-based approaches, including Logistic regression, Random forest, and Support vector machine, to facilitate the identification of microbiome markers.

Last updated 1 years ago

metagenomicsmicrobiomedifferentialexpressionbiomarker-discoverydifferential-abundance-analysislefse

6.16 score 171 stars 1 packages 188 scripts

microbiomeutilities - microbiomeutilities: Utilities for Microbiome Analytics

This is a supporting tool for extending the functionality of both phyloseq and microbiome R packages.

Last updated 2 years ago

16sampliconcore-microbiomemetagenomicsmicrobial-communitiesmicrobiomemicrobiome-analysisqc-pipelinesequencing

6.08 score 33 stars 364 scripts

MicEco - Various functions for microbial community data

Collection of functions for microbiome analyses. E.g. fitting neutral models and standardized effect sizes of phylogenetic beta diversities, and much more.

Last updated 2 years ago

16samplicon-sequencingmicrobial-communitiesmicrobial-ecologymicrobiomemicrobiome-analysisnull-model

4.15 score 41 stars 69 scripts

zAMPExplorer - zAMPExplorer: A Versatile Shiny App for Microbiota Profiling in Clinical Microbiology

A Shiny web application offering a user-friendly, accessible, and reproducible platform for downstream analysis of 16S rRNA-based metagenomics data. Key features include quality control visualizations (e.g., rarefaction curves), community composition plots, and statistical analyses for alpha- and beta-diversity. For deeper insights, the app incorporates community typing using Dirichlet multinomial modeling (DMM) and dynamically integrates metadata for sample stratification. This enables users to test microbial associations with clinical or experimental variables using redundancy analysis (RDA).

Last updated 5 hours ago

microbiologymetabarcodingvisualizationstatisticalmethod

2.60 score 1 scripts